The ecological ubiquity of parasites and their potential impacts on host behaviour have led to the suggestion that parasites can act as ecosystem engineers, structuring their environment and physical habitats. Potential modification of the relationship between parasites and their hosts by climate change has important implications for how hosts interact with both their biotic and abiotic environment. Here, we show that warming and parasitic infection independently increase rates of bioturbation by a key detritivore in aquatic ecosystems (Gammarus). These findings have important implications for ecosystem structure and functioning in a warming world, as alterations to rates of bioturbation could significantly modify oxygenation penetration and nutrient cycling in benthic sediments of rivers and lakes. Our results demonstrate a need for future ecosystem management strategies to account for parasitic infection when predicting the impacts of a warming climate.